[Bioperl-l] [Bioperl]problem with E-value

Chris Fields cjfields at uiuc.edu
Wed Jan 17 20:59:25 EST 2007


Li, Sendu,

I have committed a fix for this to CVS.  Could you check it to make  
sure everything is kosher?

The fix should work for your (Li's) BLAST report example as well as  
multiquery BLAST reports.

chris

On Jan 17, 2007, at 12:17 PM, Chris Fields wrote:

> Li, Sendu,
>
> Following up on this, I generated two new multiquery BLAST reports
> (BLASTP and BLASTX) from the NCBI BLAST server.  I can't reproduce
> output similar to Li's example (where the BLASTX header line appears
> over and over).  It is entirely possible that a local v. 2.2.15 BLAST
> installation would generate different output.
>
> Li, was the example file you sent generated from single query BLAST
> runs where the output was appended to the same file, or were they
> generated from a single BLAST run where the queries were all in one
> file?  There is a significant difference between the two.
>
> Regardless, I am able to reproduce a bug where hits aren't created
> properly from BLAST hit tables (which should be easy to fix).  I'll
> file a bug report and work on this.
>
> As a general note, if you are only interested in hits and not
> alignments you probably shouldn't use the regular BLAST text output.
> Try using -m8 -r -m9 BLAST tabular output and 'blasttable' parsing
> instead of 'blast' and maybe switch event handlers (all in the
> SearchIO HOWTO).
>
> chris
>
> On Jan 17, 2007, at 11:03 AM, Chris Fields wrote
> ...
>> ...
>> I plan on generating a new BLAST report (from the web, since I don't
>> have 2.2.15 installed) with multiple queries and no alignments to see
>> what happens (i.e. see if the new multiquery report is similar to
>> this one).  If so, there is a 'wrap-up' section of the parser, where
>> hit data not in alignments (in the table only) is used to generate
>> Hit objects; it's dropping this data likely b/c there is no regex
>> signalling the next result event.
>>
>> chris
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list